Impact of whole-genome and tandem duplications in the expansion and functional diversification of the F-box family in legumes (Fabaceae)

Abstract

F-box proteins constitute a large gene family that regulates processes from hormone signaling to stress response. F-box proteins are the substrate recognition modules of SCF E3 ubiquitin ligases. Here we report very distinct trends in family size, duplication, synteny and transcription of F-box genes in two nitrogen-fixing legumes, Glycine max (soybean) and Medicago truncatula (alfafa). While the soybean FBX genes emerged mainly through segmental duplications (including whole-genome duplications), M. truncatula genome is dominated by locally-duplicated (tandem) F-box genes. Many of these young FBX genes evolved complex transcriptional patterns, including preferential transcription in different tissues, suggesting that they have probably been recruited to important biochemical pathways (e.g. nodulation and seed development).

Figure 1. Homologous segments between V. vinifera and two legume species, G. max and M. truncatula.

The outer circle shows numbered chromosomes of each species in gray (M. truncatula, Mt), light gray (G. max, Gm) and dark gray (V. vinifera, Vv). Local duplications are represented in the second outer circle, where red denotes higher density of tandem duplications in a particular region. The line plot illustrates the number of FBX genes in each interval of 100 genes. If 5 or more FBX genes are present in a given region, the peak is colored in red. Internal arcs connect syntenic regions between V. vinifera/G. max (blue) and V. vinifera/M. truncatula (green). Colored triangles represent tandemly-duplicated FBX genes with preferential expression in late-development seeds (green), late embryogenesis seeds (red), nodules (yellow). For Gm: no detectable transcription (gray), apical meristem (green), nodule (blue), flower (yellow) and leaves (purple).

Figure 2. Transcriptional profiles of tandemly-duplicated FBX genes in G. max and M. truncatula in different tissues.

Normalized transcriptional levels were obtained from Severin at al (A) and Libault et al (B) (G. max) and Benedito et al (M. truncatula) (C) . For each independent study, gene expression values were standardized using Z-score and clustered with Hierarchical Clustering (MeV package). Numbered labels in the right refer to tandem FBX arrays (i.e. if two genes have the same number, they are very close to each other in the genome). These labels are qualitative and thus there is no correlation between label number and genomic closeness of the tandem FBX arrays.